LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants | Zendy

Mitchell J. Machiela | Zendy; Stephen J. Chanock | Zendy

Open Access

LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants

Author(s) -

Mitchell J. Machiela,

Stephen J. Chanock

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv402

Subject(s) - haplotype , pairwise comparison , linkage disequilibrium , population , single nucleotide polymorphism , biology , genetics , 1000 genomes project , association mapping , genetic association , computational biology , genome , allele , computer science , gene , genotype , artificial intelligence , demography , sociology

Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach for investigating population-specific genetic structure as well as functionally mapping regions of disease susceptibility. Here, we present LDlink, a web-based collection of bioinformatic modules that query single nucleotide polymorphisms (SNPs) in population groups of interest to generate haplotype tables and interactive plots. Modules are designed with an emphasis on ease of use, query flexibility, and interactive visualization of results. Phase 3 haplotype data from the 1000 Genomes Project are referenced for calculating pairwise metrics of LD, searching for proxies in high LD, and enumerating all observed haplotypes. LDlink is tailored for investigators interested in mapping common and uncommon disease susceptibility loci by focusing on output linking correlated alleles and highlighting putative functional variants.

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